Variant report

Variant	rs550149
Chromosome Location	chr6:143119086-143119087
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143118967..143121950-chr6:143122825..143125475,2	K562	blood:
2	chr6:143116694..143119328-chr6:143121007..143124845,4	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11155264	0.83[ASN][1000 genomes]
rs197494	0.86[JPT][hapmap]
rs197496	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs197497	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs197511	0.88[ASW][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap]
rs2328388	0.85[ASN][1000 genomes]
rs472185	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs472288	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs473497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478768	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs487754	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491414	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491953	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492156	0.89[ASN][1000 genomes]
rs494038	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs494954	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs507404	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs511565	0.85[ASN][1000 genomes]
rs512808	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs516300	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs519874	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525928	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs527870	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs533117	0.84[ASN][1000 genomes]
rs533173	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs541274	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552004	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs552928	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs557004	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs559818	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs561642	0.93[ASN][1000 genomes]
rs576657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576760	0.83[ASN][1000 genomes]
rs9386009	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9403407	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv520992	chr6:143118715-143120359	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143095800-143122200	Weak transcription	NHEK	skin
2	chr6:143096000-143122000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:143096200-143120800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:143096200-143140800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:143103600-143124800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:143103800-143125400	Weak transcription	Fetal Thymus	thymus
7	chr6:143105800-143121000	Weak transcription	Brain Angular Gyrus	brain
8	chr6:143105800-143140400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:143106000-143128200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:143106000-143140400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:143108200-143121200	Weak transcription	HSMM	muscle
12	chr6:143108400-143119400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:143108800-143123600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:143109200-143121000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:143112200-143139400	Weak transcription	HepG2	liver
16	chr6:143113200-143119400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:143113200-143140400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:143113800-143120800	Weak transcription	Pancreas	Pancrea
19	chr6:143114200-143140800	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:143116000-143121000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:143116000-143125400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:143116000-143139600	Weak transcription	Small Intestine	intestine
23	chr6:143116200-143132200	Weak transcription	Fetal Brain Female	brain
24	chr6:143117000-143129400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr6:143117000-143140800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:143117400-143119200	Weak transcription	Stomach Mucosa	stomach
27	chr6:143117600-143120400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr6:143117600-143120800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:143117600-143121400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:143117600-143122800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:143118000-143119200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:143118000-143119200	Weak transcription	Brain Anterior Caudate	brain
33	chr6:143118000-143123200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:143118000-143126200	Weak transcription	Right Ventricle	heart
35	chr6:143118000-143132200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:143118000-143137600	Weak transcription	Right Atrium	heart
37	chr6:143118200-143119200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:143118200-143119400	Weak transcription	Brain Substantia Nigra	brain
39	chr6:143118200-143119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr6:143118200-143119600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr6:143118200-143119800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr6:143118200-143120400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:143118200-143120400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:143118200-143120400	Weak transcription	Osteobl	bone
45	chr6:143118200-143120800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr6:143118200-143120800	Weak transcription	NHDF-Ad	bronchial
47	chr6:143118200-143122000	Weak transcription	Fetal Lung	lung
48	chr6:143118200-143123200	Weak transcription	Fetal Heart	heart
49	chr6:143118200-143123200	Weak transcription	HSMMtube	muscle
50	chr6:143118400-143120400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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